Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology | Zendy

Christina Weißbecker | Zendy; Beatrix Schnabel | Zendy; Anna HeintzBuschart | Zendy

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Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology

Author(s) -

Christina Weißbecker,

Beatrix Schnabel,

Anna HeintzBuschart

Publication year - 2020

Publication title -

gigascience

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 2.947

H-Index - 54

ISSN - 2047-217X

DOI - 10.1093/gigascience/giaa135

Subject(s) - computer science , amplicon sequencing , workflow , preprocessor , amplicon , pipeline (software) , data mining , process (computing) , microbial ecology , computational biology , data science , artificial intelligence , biology , database , 16s ribosomal rna , programming language , genetics , gene , polymerase chain reaction , bacteria

Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.

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